+Open data
-Basic information
Entry | Database: PDB / ID: 6oo2 | ||||||||||||
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Title | Vps4 with Cyclic Peptide Bound in the Central Pore | ||||||||||||
Components |
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Keywords | TRANSPORT PROTEIN / Vps4 / ESCRT / Vta1 / AAA ATPase | ||||||||||||
Function / homology | Function and homology information ESCRT IV complex / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / protein retention in Golgi apparatus / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / midbody abscission / vacuole organization ...ESCRT IV complex / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / protein retention in Golgi apparatus / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / midbody abscission / vacuole organization / multivesicular body sorting pathway / membrane fission / plasma membrane repair / late endosome to vacuole transport / multivesicular body assembly / reticulophagy / nucleus organization / lipid transport / endosomal transport / ATPase complex / ATPase activator activity / autophagosome maturation / nuclear pore / multivesicular body / macroautophagy / autophagy / protein-macromolecule adaptor activity / protein transport / midbody / endosome / endoplasmic reticulum / ATP hydrolysis activity / protein homodimerization activity / ATP binding / membrane / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||||||||
Authors | Han, H. / Fulcher, J.M. / Dandey, V.P. / Sundquist, W.I. / Kay, M.S. / Shen, P. / Hill, C.P. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Elife / Year: 2019 Title: Structure of Vps4 with circular peptides and implications for translocation of two polypeptide chains by AAA+ ATPases. Authors: Han Han / James M Fulcher / Venkata P Dandey / Janet H Iwasa / Wesley I Sundquist / Michael S Kay / Peter S Shen / Christopher P Hill / Abstract: Many AAA+ ATPases form hexamers that unfold protein substrates by translocating them through their central pore. Multiple structures have shown how a helical assembly of subunits binds a single ...Many AAA+ ATPases form hexamers that unfold protein substrates by translocating them through their central pore. Multiple structures have shown how a helical assembly of subunits binds a single strand of substrate, and indicate that translocation results from the ATP-driven movement of subunits from one end of the helical assembly to the other end. To understand how more complex substrates are bound and translocated, we demonstrated that linear and cyclic versions of peptides bind to the AAA+ ATPase Vps4 with similar affinities, and determined cryo-EM structures of cyclic peptide complexes. The peptides bind in a hairpin conformation, with one primary strand equivalent to the single chain peptide ligands, while the second strand returns through the translocation pore without making intimate contacts with Vps4. These observations indicate a general mechanism by which AAA+ ATPases may translocate a variety of substrates that include extended chains, hairpins, and crosslinked polypeptide chains. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6oo2.cif.gz | 388.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oo2.ent.gz | 306.3 KB | Display | PDB format |
PDBx/mmJSON format | 6oo2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/6oo2 ftp://data.pdbj.org/pub/pdb/validation_reports/oo/6oo2 | HTTPS FTP |
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-Related structure data
Related structure data | 20142MC 0443C 6ndyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Vacuolar protein sorting-associated protein ... , 2 types, 18 molecules ABCDEFHIJKLMNOPQRS
#1: Protein | Mass: 37120.750 Da / Num. of mol.: 6 / Fragment: UNP residues 101-437 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: VPS4, CSC1, DID6, END13, GRD13, VPL4, VPT10, YPR173C, P9705.10 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P52917 #3: Protein | Mass: 5773.649 Da / Num. of mol.: 12 / Fragment: VSL domain (UNP residues 280-330) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: VTA1, YLR181C Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q06263 |
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-Protein/peptide , 1 types, 1 molecules G
#2: Protein/peptide | Mass: 2660.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 3 types, 12 molecules
#4: Chemical | ChemComp-ADP / #5: Chemical | #6: Chemical | ChemComp-MG / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Vps4-Vta1 with a Cyclic peptide binding to the central pore Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 76.68 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24778 / Symmetry type: POINT |